A small detail when use VEP

Question

[Laven9]

It is a small question I met when running vcf2maf (VEP): If you run vcf2maf (VEP), there is a fasta file needed to be offered. And my question is: since I used hg38.fa for my previous work, which fasta file should I give? hg38.fa or Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz from VEP? As researched, I got the notion that the difference between hg38 and GRCh38 is only the contigs like chrx VS x, so I suppose it doesn't matter and I could choose either of the two. Am I right?

Answer 1

[WouterDeCoster]

the difference between hg38 and GRCh38 is only the contigs like chrx VS x, so I suppose it doesn't matter and I could choose either of the two

I don't know for this tool (vcf2maf) specifically, but it definitely does matter for most tools. Always use the same reference for one project. If you used hg38.fa for alignment, then stick to it.

[Laven9]

I see your point! Thank you for your advice!